find_format {qckitfastq} | R Documentation

## Gets quality score encoding format from the FASTQ file. Return possibilities are Sanger(/Illumina1.8), Solexa(/Illumina1.0), Illumina1.3, and Illumina1.5. This encoding is heuristic based and may not be 100 since there is overlap in the encodings used, so it is best if you already know the format.

### Description

Gets quality score encoding format from the FASTQ file. Return possibilities are Sanger(/Illumina1.8), Solexa(/Illumina1.0), Illumina1.3, and Illumina1.5. This encoding is heuristic based and may not be 100 since there is overlap in the encodings used, so it is best if you already know the format.

### Usage

    find_format(infile, reads_used)

### Arguments

`infile` | A string giving the path for the fastq file
`reads_used` | int, the number of reads to use to determine the encoding format.

### Value

A string denoting the read format. Possibilities are Sanger, Solexa, Illumina1.3, and Illumina1.5.

### Examples

    infile <- system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq")
    find_format(infile,100)

[Package qckitfastq version 1.6.0 Index]